Grease Pencil animation rendering only the background
In order to render a grease pencil animation, you have to use OpenGL render.  Using the blend file that you provided, if you open it, up there are two views, 
directly under the view that you want to render there is a plus


If you click that and then scroll to the right by dragging the middle mouse over the bottom section(the panel menu) you will see the OpenGL render button.



The one on the left renders the current frame and the one on the right renders the animation.  Just make sure that you deselect everything before you render as it is just rendering the viewport at a higher resolution.